This volume addresses a variety of areas in which computers are used to manage and manipulate nucleic acid and protein sequence data. The manipulations include searching, aligning, and determining the significance of similarities, as well as the construction of phylogenetic trees that show the evolutionary history of related sequences. Ready-to-use methods for the "at-the-bench" scientist are presented.


Biochemists, molecular biologists, evolutionary biologists, geneticists, cell biologists, and biotechnologists.

Table of Contents

Databases: C. Burks et al. , GenBank: Current Status and Future Directions. P. Kahn and G. Cameron, EMBL Data Library. W.C. Barker, D.G. George, and L.T. Hunt, Protein Sequence Database. B. Keil, Cooperation between Databases and Scientific Community. Searching Databases: W.R. Pearson, Rapid and Sensitive Sequence Comparison with FASTP and FASTA. R.F. Doolittle, Searching through Sequence Databases. S. Henikoff, J.C. Wallace, and J.P. Brown, Finding Protein Similarities with Nucleotide Sequence Databases. C.B. Lawrence, Use of Homology Domains in Sequence Similarity Detection. M. Gribskov, R. L~aduthy, and D. Eisenberg, Profile Analysis. Patterns in Nucleic Acid Sequences: R. Staden, Finding Protein Coding Regions in Genomic Sequences. J.C.W. Shepherd, Ancient Patterns in Nucleic Acid Sequences. R. Staden, Searching for Patterns in Protein and Nucleic Acid Sequences. G.D. Stormo, Consensus Patterns in DNA. M.S. Waterman and R. Jones, Consensus Methods for DNA and Protein Sequence Alignment. J.-M. Claverie, I. Sauvaget, and L. Bougueleret, k-Tuple Frequency Analysis: From Intron/Exon Discrimination to T-Cell Epitope Mapping. P. Senapathy, M.B. Shapiro, and N.L. Harris, Splice Junctions, Branch Point Sites, and Exons: Sequence Statistics, Identification, and Applications to Genome Project. Predicting RNA Secondary Structures: J.A. Jaeger, D.H. Turner, and M. Zuker, Predicting Optimal and Suboptimal Secondary Structure for RNA. H.M. Martinez, Detecting Pseudoknot


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© 1990
Academic Press
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